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InterPro Ids in GOA association file? Is it needed?

Suzanna Lewis suzi at fruitfly.org
Mon Nov 28 13:30:56 PST 2005


Exactly. I also think these belong in column 8.

On Nov 28, 2005, at 11:46 AM, David Hill wrote:

> Suzi and Evelyn,
>
> I also don't see why this can't just go in column 8 since the interpro 
> ID would be a valid dbxref. This is what we did with the original 
> fantom data.
>
> David
>
> Suzanna Lewis wrote:
>
>>
>> On Nov 28, 2005, at 6:26 AM, Evelyn Camon wrote:
>>
>>> Dear GO friends,
>>>
>>> We have been discussing here at EBI whether we should include the 
>>> InterProID in our association files so that users of this file could 
>>> quickly deduce the exact InterProID source of the annotation.
>>>
>>> At the moment we use GOA:interPro in the 6th column of the 
>>> association file called DB:Reference. We also add to this column for 
>>> manual annotation PUBMED:9058808, for other IEA annotations 
>>> GOA:hamap, GOA:spkw, GOA:spec.
>>
>>
>> If you are now doing this already what is the new thing you are 
>> proposing?
>>
>> Since Interpro matches are how you are determining the GO assignment 
>> I wonder why you aren't using the with column (column 8) for the 
>> interpro ID?
>>
>>>
>>> I understand that adding this information would expand the size of 
>>> the association file we produce and slow down our release procedure. 
>>> We are wondering whether this would be a hinderance and if indeed it 
>>> is widely useful or not. Do most people prefer to apply the 
>>> InterPro2go mapping to there datasets or are they using other 
>>> computing means to link
>>> UniProt AC->InterProID->GO:ID. If they were having difficulty with 
>>> the latter we could produce UniProt AC->InterProID->GO:ID as an 
>>> extra file perhaps.
>>
>>
>> please do not create an extra file.
>>
>>>
>>> We would very much like to know how this would affect GO Tools and GO
>>> Consortium members that download our data and if it would be useful 
>>> or not. Please feedback to us anything that you would consider an 
>>> approvement to our services.
>>>
>>> kind regards
>>> Evelyn Camon
>>> GOA-Coordinator
>>>
>>>
>>> -- 
>>> This message is from the GOFriends moderated mailing list.  A list 
>>> of public
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>>
>>
>>
>> -- 
>> This message is from the GOFriends moderated mailing list.  A list of 
>> public
>> announcements and discussion of the Gene Ontology (GO) project.
>> Problems with the list?           E-mail: 
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>
>
>
> -- 
> David P. Hill, Ph.D.
> Senior Scientific Curator
> Mouse Genome Informatics
> Gene Ontology Consortium
> Gene Expression Database
> The Jackson Laboratory
> 600 Main Street
> Bar Harbor, ME 04609-1500
> tel:207-288-6430
> htpp://www.informatics.jax.org
>


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